First you need to update the DSTwo. Get both the latest EOS and the latest firmware file and extract them to the root of the SD card (i.e. X:\). After that, put it in your DS Lite, turn it on, and say yes when it wants to update.

Second, you will need to get the plugins. I suggest getting the GBA and SNES ones to start. For the GBA one it is important to get version 1.21 and NOT 1.30 as 1.30 breaks a few things. For SNES I suggest using CATSFC. For plugins there will usually be both a plugin data folder (NDSGBA/CATSCF) which goes in the root and either a .ini and .plg file or a _dstwoplug folder containing a .plg/.ini file. Both the .plg and .ini files go in X:\_dstwoplug

Finally, DS games can go anywhere though I suggest making a DS_Games folder and then dividing the games into subfolders (i.e. X:\DS_Games\RPGs or X:\DS_Games\AtoM).